The subtropical archipelago of Okinawa (SW The subtropical archipelago of Okinawa (SW Japan) hosts the biggest coral reef in Japan with high biodiversity and endemism. However, its reefs are subjected to multiple pressures. Changes in reefs’ community composition need to be tracked implementing current monitoring systems that are mainly observer-based. In recent years, different studies tested the use of environmental DNA and metabarcoding together with traditional monitoring techniques. 

Compared to traditional methods, the eDNA metabarcoding approach has many practical advantages such as being non-invasive, time-, and cost-efficient. In terms of results, it allows the characterization of a wider spectrum of organisms present in biological communities, including microbes; moreover, it facilitates the detection of cryptic and nocturnal species. It has also been applied for early detections of alien species. 

To gather information on the composition of metazoan assemblages at each of the 12 surveyed sites in Okinawa, a primer targeting COI was used for eDNA amplification from water samples. 

The project has three main objectives: 

a) characterize differences in community composition and functions among impacted and “pristine” sites; 

b) observe the differences in community composition and impacts at different depths; 

c) assess whether the eDNA signal is localized and how it changes with distance among different sites.

ABSTRACT:

Coral reefs are extremely biodiverse and productive marine ecosystems, but they are vulnerable to anthropogenic pressures, and shifts in their structure and community compositions have been observed. The subtropical Ryukyu Archipelago of southern Japan hosts the largest coral reefs of the country, and they are characterized by high biodiversity; however, some reefs, especially around Okinawajima Island, are degraded. Monitoring and impact assessments in this region are scattered, and most studies have focused on a single disturbance and/or a single taxon. A benthic multi-taxa survey protocol was tested at four locations exposed to different levels of anthropogenic pressures along Okinawajima and Akajima islands. Data from Line Intercept Transects (relative benthic cover, and algae and hard coral cover by functional groups) were integrated with echinoderm and mollusk abundance by class. Only the remote island of Akajima seemed not to be highly degraded with hard corals dominant. The results suggested that Echinoidea and Bivalvia abundances could be good indicators to discriminate among sites. The monitoring protocol was rapid, cheap, and effective in highlighting differences in benthic composition between pristine and impacted sites; thus, this method can be deployed at a large scale, contributing to urgently needed reef conservation and management.